Physarum Time-Series to Zarr
Run this script
uv run https://atrium.kyleharrington.com/laboratory/convert_physarum_to_zarr/main.py
Command Line Arguments
--image_path
(str)
--output_path
(str)
Path to save visualization
--rows
(int)
Number of rows in dish layout
Default: 3
--cols
(int)
Number of columns in dish layout
Default: 2
--margin_factor
(float)
Margin factor for dish detection
Default: 0.03
--downsample_ratio
(float)
Downsample ratio for processing
Default: 0.5
--pad_radius
(int)
Additional padding in pixels to add to dish radius
Default: 0
--input_dir
(str)
--output_path
(str)
--chunk_size
(str)
Chunk size as comma-separated values
Default: 10,1,400,400,3
--rows
(int)
Number of rows in dish layout
Default: 3
--cols
(int)
Number of columns in dish layout
Default: 2
--apply_mask
(bool)
Apply circular dish masking
Default: True
--margin_factor
(float)
Margin factor for dish detection
Default: 0.03
--downsample_ratio
(float)
Downsample ratio for processing
Default: 0.5
--sample_interval
(int)
Interval for checking dish position consistency
Default: 10
--pad_radius
(int)
Additional padding in pixels to add to dish radius
Default: 0
--zarr_path
(str)
--image_path
(str)
--dish_index
(int)
Index of the dish to test (0-5)
Default: 0
--rows
(int)
Number of rows in dish layout
Default: 3
--cols
(int)
Number of columns in dish layout
Default: 2
--margin_factor
(float)
Margin factor for dish detection
Default: 0.03
--downsample_ratio
(float)
Downsample ratio for processing
Default: 0.5
--pad_radius
(int)
Additional padding in pixels to add to dish radius
Default: 0
--save_path
(str)
Path to save visualization (optional)
Dependencies
- zarr>=2.15.0,<3
- numpy>=1.24.0
- pillow>=10.0.0
- tqdm>=4.65.0
- typer>=0.9.0
- opencv-python>=4.8.0
- scikit-image>=0.21.0
- matplotlib>=3.7.0